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arXiv · 2003.11817

Estimation of genome size using k-mer frequencies from corrected long reads

Hengchao Wang·Bo Liu·Yan Zhang·Fan Jiang·Yuwei Ren·Lijuan Yin·Hangwei Liu·Sen Wang·Wei Fan
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Abstract

The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy, third-generation sequencing data cannot be used for k-mer counting and estimating genomic profile based on k-mer frequencies. Thus, in current genome projects, second-generation data is also necessary for accurately determining genome size and other genomic characteristics. We show that corrected third-generation data can be used to count k-mer frequencies and estimate genome size reliably, in replacement of using second-generation data. Therefore, future genome projects can depend on only one sequencing technology to finish both assembly and k-mer analysis, which will largely decrease sequencing cost in both time and money. Moreover, we present a fast light-weight tool kmerfreq and use it to perform all the k-mer counting tasks in this work. We have demonstrated that corrected third-generation sequencing data can be used to estimate genome size and developed a new open-source C/C++ k-mer counting tool, kmerfreq, which is freely available at https://github.com/fanagislab/kmerfreq.

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Hengchao Wang, Bo Liu, Yan Zhang, Fan Jiang, Yuwei Ren, Lijuan Yin, Hangwei Liu, Sen Wang, Wei Fan. 2020-03-26. Estimation of genome size using k-mer frequencies from corrected long reads. https://arxiv.org/abs/2003.11817

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